i didn't change anything on the image other than made sure it had an alpha channel (in GIMP, adding it to the layer doesn't give the image an alpha transprency, you have to bring in a transprent layer under it as well then export as a tga)


your leaf image applied to a 4 poly flat model

i placed in 2 of them to check for sorting. worked fine


So here are some possible problems you might be having, that i can think of.....
your not actualy getting an alpha channel into your skin or not saving it as a 32 bit image
your tree models polygon faces have been inverted/flipped ( face inwards)
your setting some flag on your model that effects transparency ( overlay, transparent, flare...)
the models polygons are too small in many spots and may be being clipped ( not likely but can happen)